Update readme

Quick and dirty hack to allow imagej (python) scripts to open hdf5 files via a routine and do operation with them.
This is far from perfect and needs major cleanup! It is implemented like this due to lack of time ...

.gitignore

@@ -1,3 +1,4 @@
+.idea
 /target
 .gradle
 build

Readme.md

@@ -1,4 +1,4 @@
-# Overview
+ # Overview
 
 ImageJ plugin for reading and writing HDF5 files.
 
@@ -20,6 +20,16 @@ To save to an HDF5 file use:
 File > SaveAs > HDF5
 ```
 
+## Scripting
+
+To use this plugin from the ImageJs' (python) scripting interface these lines can be used to open a dataset:
+
+```python
+from ch.psi.imagej.hdf5 import HDF5Reader
+reader = HDF5Reader()
+stack = reader.open("",False, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchange/data_dark", True)
+```
+
 # Installation
 To be able to install this plugin ImageJ need to be run with a Java 7 or greater JVM.
 
@@ -79,6 +89,11 @@ cd <FIJI_HOME>
 Starting with Java 8 just the LD_LIBRARY_PATH variable need to be set. For MacOSX it is export `DYLD_LIBRARY_PATH=lib/mac64/:$DYLD_LIBRARY_PATH`.
 
 # Development
+
+To be able to run the tests and plugin from within the following arguments need to be passed:
+
+![RunSettings](RunSettings.png)
+
 To create an all in one zip file for installation in a ImageJ installation use: 
 `mvn clean compile assembly:assembly`
 

build.gradle

@@ -2,7 +2,7 @@ apply plugin: 'java'
 apply plugin: 'maven'
 
 group = 'ch.psi'
-version = '0.8.0'
+version = '0.11.0'
 
 description = """"""
 
@@ -13,7 +13,7 @@ targetCompatibility = 1.7
 
 repositories {
      mavenCentral()
-     maven { url "http://slsyoke4.psi.ch:8081/artifactory/libs-releases" }
+     maven { url "http://artifacts.psi.ch/artifactory/libs-releases" }
 }
 dependencies {
     compile group: 'hdf5', name: 'hdf', version:'2.10.0'

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>imagej.hdf5</artifactId>
-	<version>0.9.0</version>
+	<version>0.11.0</version>
 
 	<dependencies>
 		<dependency>

src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java

@@ -10,7 +10,7 @@ import ij.plugin.PlugIn;
 
 import java.io.File;
 import java.lang.reflect.Array;
-import java.util.List;
+import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -28,45 +28,83 @@ public class HDF5Reader implements PlugIn {
 	 */
 	public static void main(String[] args){
 		HDF5Reader r = new HDF5Reader();
-		r.run("");
+//		r.run("");
+		r.open("",false, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchange/data", true);
 	}
-	
+
+	public void run(String arg) {
+		open(arg, true, null, null, true);
+	}
+
 	/**
 	 * Main function plugin
+	 * arg is a space separated list of arguments that can be passed to the run method.
+	 * arg looks something like this: "para1=value1 para2=value2 ....."
+	 *
+	 * Supported arguments for arg:
+	 * open=<path>
+	 * dataset=/your/path/to/dataset
+	 *
 	 */
-	public void run(String arg) {
+	public ImageStack open(String arg, boolean interactive, String filename, String nameOfDataset, boolean virtualstack) {
 
-		OpenDialog od = new OpenDialog("Open HDF5 ...", arg);
+//		Map arguments = HDF5Reader.parseArguments(arg);
 
-		
+		File tfile = null;
-		File tfile = new File(od.getDirectory() + od.getFileName());
+		if(interactive) {
-		if (!tfile.exists() || !tfile.canRead()) {
+			OpenDialog od = new OpenDialog("Open HDF5 ...", arg);
-			IJ.showMessage("Cannot open file: "+tfile.getAbsolutePath());
+			tfile = new File(od.getDirectory() + od.getFileName());
-			return;
+			if (!tfile.exists() || !tfile.canRead()) {
+				IJ.showMessage("Cannot open file: "+tfile.getAbsolutePath());
+				return null;
+			}
+
+			// Overwrite filename with selected filename
+			filename = tfile.getAbsolutePath();
+
+			IJ.showStatus("Loading HDF5 File: " + filename);
+			IJ.showProgress(0.0);
 		}
-		String filename = tfile.getAbsolutePath();
-
-		IJ.showStatus("Loading HDF5 File: " + filename);
-		IJ.showProgress(0.0);
 		
 		// Read HDF5 file
 		H5File file = null;
 		boolean close = true;
+
+		List<ImageStack> stacks = new ArrayList<>();
+		ImageStack stack = null;
+
 		try {
 			file = new H5File(filename, H5File.READ);
 			file.setMaxMembers(Integer.MAX_VALUE);
 			file.open();
 
 			List<Dataset> datasets = HDF5Utilities.getDatasets(file);
-			DatasetSelection selectedDatasets = selectDatasets(datasets);
+
+			DatasetSelection selectedDatasets = null;
+			if(interactive){
+				logger.info("Using manual selection");
+				// Manual selection of the dataset and other parameters via a dialog
+				selectedDatasets = selectDatasets(datasets);
+			}
+			else{
+				logger.info("Using automatic selection");
+				selectedDatasets = new DatasetSelection();
+				for(Dataset dataset: datasets){
+					if(dataset.getFullName().equals(nameOfDataset)){
+						selectedDatasets.getDatasets().add(dataset);
+						break; // we only support one selection for the time being
+					}
+				}
+				selectedDatasets.setVirtualStack(virtualstack);
+			}
+
+
 			// TODO to be removed - Workaround virtual stack - keep HDF5 file open at the end 
 			close=!selectedDatasets.isVirtualStack();
 
-			
 			// TODO Remove
 			// Hack as a proof of principle
 			if(selectedDatasets.isGroup()){
-				ImageStack stack = null;
 				
 				for (Dataset var : selectedDatasets.getDatasets()) {
 					if(stack == null){
@@ -81,10 +119,11 @@ public class HDF5Reader implements PlugIn {
 				ImagePlus imp = new ImagePlus(filename, stack);
 				imp.resetDisplayRange();
 				imp.show();
-				return;
+
+				stacks.add(stack);
+				return stack; // TODO should return stacks instead of stack
 			}
-			
+
-			
 			for (Dataset var : selectedDatasets.getDatasets()) {
 
 				// Read dataset attributes and properties
@@ -111,7 +150,8 @@ public class HDF5Reader implements PlugIn {
 
 					Object wholeDataset = var.read();
 
-					ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
+					stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
+					stacks.add(stack);
 					int stackSize = (int) (dimensions[2] * dimensions[3] * 3);
 					int singleVolumeSize = (int) (dimensions[1] * stackSize);
 					for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
@@ -141,7 +181,8 @@ public class HDF5Reader implements PlugIn {
 
 					Object wholeDataset = var.read();
 
-					ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
+					stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
+					stacks.add(stack);
 					int stackSize = (int) (dimensions[1] * dimensions[2] * 3);
 					for (int lev = 0; lev < dimensions[0]; ++lev) {
 						int startIdx = lev * stackSize;
@@ -168,7 +209,8 @@ public class HDF5Reader implements PlugIn {
 
 					Object wholeDataset = var.read();
 
-					ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
+					stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
+					stacks.add(stack);
 					int size = (int) (dimensions[2] * dimensions[3]);
 					long singleVolumeSize = dimensions[1] * size;
 					for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
@@ -196,7 +238,8 @@ public class HDF5Reader implements PlugIn {
 
 					Object wholeDataset = var.read();
 
-					ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
+					stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
+					stacks.add(stack);
 					addSliceRGB(stack, wholeDataset, (int) dimensions[0], (int) dimensions[1]);
 
 					ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
@@ -209,8 +252,6 @@ public class HDF5Reader implements PlugIn {
 				} else if (numberOfDimensions == 3) {
 					logger.info("3D Image");
 
-					ImageStack stack;
-					
 					if(selectedDatasets.isVirtualStack()){
 						logger.info("Use virtual stack");
 						stack = new VirtualStackHDF5(file, var);
@@ -278,6 +319,7 @@ public class HDF5Reader implements PlugIn {
 						}
 					}
 
+					stacks.add(stack);
 					ImagePlus imp = new ImagePlusHDF5(filename + " " + datasetName, stack);
 					imp.resetDisplayRange();
 					imp.show();
@@ -287,7 +329,8 @@ public class HDF5Reader implements PlugIn {
 					
 					Object wholeDataset = var.read();
 
-					ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
+					stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
+					stacks.add(stack);
 					addSlice(stack, wholeDataset);
 					
 					ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
@@ -319,6 +362,8 @@ public class HDF5Reader implements PlugIn {
 		}
 
 		IJ.showProgress(1.0);
+
+		return stack; // TODO should return stacks instead of stack
 	}
 
 	/**
@@ -353,7 +398,6 @@ public class HDF5Reader implements PlugIn {
 		return selectedDatasets;
 	}
 
-
 	/**
 	 * Add slice to image stack
 	 * @param stack		Stack to add slice
@@ -433,4 +477,22 @@ public class HDF5Reader implements PlugIn {
 		stack.addSlice(null, g);
 		stack.addSlice(null, b);
 	}
+
+	public static Map<String,String> parseArguments(String arg){
+
+		/// ImageJ arguments look something like this: "para1=value1 para2=value2 ....."
+		Map<String,String> map = new HashMap<>();
+		arg = arg.trim();
+		for(String argument: arg.split("\\s+")){
+			String[] entry = argument.split("=");
+			if(entry.length==2) {
+				map.put(entry[0], entry[1]);
+			}
+			else{
+				// ignore
+				logger.warning("Cannot parse argument " + argument + " - Ignore");
+			}
+		}
+		return map;
+	}
 }

src/main/java/ch/psi/imagej/hdf5/ImagePlusHDF5.java

@@ -29,32 +29,32 @@ public class ImagePlusHDF5 extends ImagePlus {
 			
 			@Override
 			public void windowOpened(WindowEvent e) {
-				logger.info("");
+//				logger.info("");
 			}
 			
 			@Override
 			public void windowIconified(WindowEvent e) {
-				logger.info("");
+//				logger.info("");
 			}
 			
 			@Override
 			public void windowDeiconified(WindowEvent e) {
-				logger.info("");
+//				logger.info("");
 			}
 			
 			@Override
 			public void windowDeactivated(WindowEvent e) {
-				logger.info("");
+//				logger.info("");
 			}
 			
 			@Override
 			public void windowClosing(WindowEvent e) {
-				logger.info("Closing");
+//				logger.info("Closing");
 			}
 			
 			@Override
 			public void windowClosed(WindowEvent e) {
-				logger.info("Closed");
+//				logger.info("Closed");
 				
 				if(stack!=null){
 					stack.close();
@@ -63,7 +63,7 @@ public class ImagePlusHDF5 extends ImagePlus {
 			
 			@Override
 			public void windowActivated(WindowEvent e) {
-				logger.info("");
+//				logger.info("");
 			}
 		});
 	}

src/test/java/ch/psi/imagej/hdf5/HDF5ReaderTest.java

@@ -0,0 +1,22 @@
+package ch.psi.imagej.hdf5;
+
+import org.junit.Test;
+
+import java.util.Map;
+
+import static org.junit.Assert.*;
+
+/**
+ *
+ */
+public class HDF5ReaderTest {
+    @Test
+    public void parseArguments() throws Exception {
+
+        Map map = HDF5Reader.parseArguments("para1=value1 para2=value2  PARA=VAL");
+        assertTrue(map.get("para1").equals("value1"));
+        assertTrue(map.get("para2").equals("value2"));
+        assertTrue(map.get("PARA").equals("VAL"));
+    }
+
+}

src/test/java/ch/psi/imagej/hdf5/HDF5UtilitiesTest.java

@@ -2,6 +2,7 @@ package ch.psi.imagej.hdf5;
 
 import static org.junit.Assert.*;
 
+import ij.IJ;
 import org.junit.Test;
 
 public class HDF5UtilitiesTest {
@@ -22,4 +23,14 @@ public class HDF5UtilitiesTest {
 		assertEquals(gdescriptor, "three");
 	}
 
+
+	@Test
+	public void testOpen() {
+		IJ.run("HDF5...");
+		String descriptor = "/test/one/two/three";
+		String gdescriptor = HDF5Utilities.getDatasetName(descriptor);
+		System.out.println(gdescriptor);
+		assertEquals(gdescriptor, "three");
+	}
+
 }